General Genetics questions

8/19/2019 General Genetics questions

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Question 2

The DNA sequence of phenylalanine hydroxylase known as PAH gene are presence in the

Homo sapiens gene which it produces the enzyme PAH for processing the phenylalanine for building the block of amino acid which obtained through the diet and this can be found in all

proteins content and some in artificial sweeteners. The phenylalanine hydroxylase is

responsible for the conversion of the phenylalanine into another amino acid which is tyrosine.

This enzyme carries out the function with a molecule called tetrahydrobiopterin known as

BH4 to carry out its chemical reaction.

The PAH gene can be found and located cytogenetic location !"q""#q"$." and the molecular

location on the chromosome !" is base pairs !%"&'('&("! to !%"&)!*&+%( (Homo sapiens

Annotation Release 107, GRCh38.p2)

,ased on the figure above the PAH gene is located on the long -q arm of chromosome !"

between "" and "$." which is more precisely at base pair !%"&'('&("! to base pair

!%"&)!*&+%( at chromosome !".

/n order to identify the DNA coding sequence of the Homo sapiens phenylalaninehydroxylase - PAH gene we use the restriction enzyme of Noa!"ia o!allina (No#) to

identify the restriction site that can be recognized in the PAH sequence which we listed the

whole PAH sequence in figure below.


2/9

Homo sapiens phenylalanine hydroxylase (PAH), mRNA

2680 base pairs

cagctgggggtaaggggggcggattattcatataattgttataccagacggtcgcaggcttagtccaattgcaga

base pairs

gtcgacccccattccccccgcctaataagtatattaacaatatggtctgccagcgtccgaatcaggttaacgtct

1 to 75

gaactcgcttcccaggcttctgagagtcccggaagtgcctaaacctgtctaatcgacggggcttgggtggcccgt

base pairs

cttgagcgaagggtccgaagactctcagggccttcacggatttggacagattagctgccccgaacccaccgggca

76 to 150

cgctccctggcttcttccctttacccagggcgggcagcgaagtggtgcctcctgcgtcccccacaccctccctca

base pairs

gcgagggaccgaagaagggaaatgggtcccgcccgtcgcttcaccacggaggacgcagggggtgtgggagggagt

151 to 225

gcccctcccctccggcccgtcctgggcaggtgacctggagcatccggcaggctgccctggcctcctgcgtcagga

base pairs

cggggaggggaggccgggcaggacccgtccactggacctcgtaggccgtccgacgggaccggaggacgcagtcct

226 to 300

caagcccacgaggggcgttactgtgcggagatgcaccacgcaagagacaccctttgtaactctcttctcctccct

base pairs

gttcgggtgctccccgcaatgacacgcctctacgtggtgcgttctctgtgggaaacattgagagaagaggaggga

301 to 375


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agtgcgaggttaaaaccttcagccccacgtgctgtttgcaaacctgcctgtacctgaggccctaaaaagccagag

base pairs

tcacgctccaattttggaagtcggggtgcacgacaaacgtttggacggacatggactccgggatttttcggtctc

376 to 450

acctcactcccggggagccagcatgtccactgcggtcctggaaaacccaggcttgggcaggaaactctctgactt

base pairs

tggagtgagggcccctcggtcgtacaggtgacgccaggaccttttgggtccgaacccgtcctttgagagactgaa

451 to 525

tggacaggaaacaagctatattgaagacaactgcaatcaaaatggtgccatatcactgatcttctcactcaaaga

base pairs

acctgtcctttgttcgatataacttctgttgacgttagttttaccacggtatagtgactagaagagtgagtttct

526 to 600

agaagttggtgcattggccaaagtattgcgcttatttgaggagaatgatgtaaacctgacccacattgaatctag

base pairs

tcttcaaccacgtaaccggtttcataacgcgaataaactcctcttactacatttggactgggtgtaacttagatc

601 to 675

accttctcgtttaaagaaagatgagtatgaatttttcacccatttggataaacgtagcctgcctgctctgacaaa

base pairs

tggaagagcaaatttctttctactcatacttaaaaagtgggtaaacctatttgcatcggacggacgagactgttt

676 to 750

catcatcaagatcttgaggcatgacattggtgccactgtccatgagctttcacgagataagaagaaagacacagt

base pairs

gtagtagttctagaactccgtactgtaaccacggtgacaggtactcgaaagtgctctattcttctttctgtgtca

751 to 825


4/9

gccctggttcccaagaaccattcaagagctggacagatttgccaatcagattctcagctatggagcggaactgga

base pairscgggaccaagggttcttggtaagttctcgacctgtctaaacggttagtctaagagtcgatacctcgccttgacct

826 to 900

tgctgaccaccctggttttaaagatcctgtgtaccgtgcaagacggaagcagtttgctgacattgcctacaacta

base pairs

acgactggtgggaccaaaatttctaggacacatggcacgttctgccttcgtcaaacgactgtaacggatgttgat

901 to 975

NcoI

ccgccatgggcagcccatccctcgagtggaatacatggaggaagaaaagaaaacatggggcacagtgttcaagac

base pairs

ggcggtacccgtcgggtagggagctcaccttatgtacctccttcttttcttttgtaccccgtgtcacaagttctg

976 to 1050

tctgaagtccttgtataaaacccatgcttgctatgagtacaatcacatttttccacttcttgaaaagtactgtgg

base pairs

agacttcaggaacatattttgggtacgaacgatactcatgttagtgtaaaaaggtgaagaacttttcatgacacc

1051 to 1125

cttccatgaagataacattccccagctggaagacgtttctcaattcctgcagacttgcactggtttccgcctccg

base pairs

gaaggtacttctattgtaaggggtcgaccttctgcaaagagttaaggacgtctgaacgtgaccaaaggcggaggc

1126 to 1200

acctgtggctggcctgctttcctctcgggatttcttgggtggcctggccttccgagtcttccactgcacacagta


5/9

base pairs

tggacaccgaccggacgaaaggagagccctaaagaacccaccggaccggaaggctcagaaggtgacgtgtgtcat

1201 to 1275

catcagacatggatccaagcccatgtatacccccgaacctgacatctgccatgagctgttgggacatgtgccctt

base pairs

gtagtctgtacctaggttcgggtacatatgggggcttggactgtagacggtactcgacaaccctgtacacgggaa

1276 to 1350

gttttcagatcgcagctttgcccagttttcccaggaaattggccttgcctctctgggtgcacctgatgaatacat

base pairs

caaaagtctagcgtcgaaacgggtcaaaagggtcctttaaccggaacggagagacccacgtggactacttatgta

1351 to 1425

tgaaaagctcgccacaatttactggtttactgtggagtttgggctctgcaaacaaggagactccataaaggcata

base pairs

acttttcgagcggtgttaaatgaccaaatgacacctcaaacccgagacgtttgttcctctgaggtatttccgtat

1426 to 1500

tggtgctgggctcctgtcatcctttggtgaattacagtactgcttatcagagaagccaaagcttctccccctgga

base pairs

accacgacccgaggacagtaggaaaccacttaatgtcatgacgaatagtctcttcggtttcgaagagggggacct

1501 to 1575

gctggagaagacagccatccaaaattacactgtcacggagttccagcccctgtattacgtggcagagagttttaa

base pairs

cgacctcttctgtcggtaggttttaatgtgacagtgcctcaaggtcggggacataatgcaccgtctctcaaaatt

1576 to 1650


6/9

tgatgccaaggagaaagtaaggaactttgctgccacaatacctcggcccttctcagttcgctacgacccatacac

base pairs

actacggttcctctttcattccttgaaacgacggtgttatggagccgggaagagtcaagcgatgctgggtatgtg1651 to 1725

ccaaaggattgaggtcttggacaatacccagcagcttaagattttggctgattccattaacagtgaaattggaat

base pairs

ggtttcctaactccagaacctgttatgggtcgtcgaattctaaaaccgactaaggtaattgtcactttaacctta

1726 to 1800

NcoI

cctttgcagtgccctccagaaaataaagtaaagccatggacagaatgtggtctgtcagctgtgaatctgttgatg

base pairs

ggaaacgtcacgggaggtcttttatttcatttcggtacctgtcttacaccagacagtcgacacttagacaactac

1801 to 1875

gagatccaactatttctttcatcagaaaaagtccgaaaagcaaaccttaatttgaaataacagccttaaatcctt

base pairs

ctctaggttgataaagaaagtagtctttttcaggcttttcgtttggaattaaactttattgtcggaatttaggaa

1876 to 1950

tacaagatggagaaacaacaaataagtcaaaataatctgaaatgacaggatatgagtacatactcaagagcataa

base pairs

atgttctacctctttgttgtttattcagttttattagactttactgtcctatactcatgtatgagttctcgtatt

1951 to 2025

tggtaaatcttttggggtcatctttgatttagagatgataatcccatactctcaattgagttaaatcagtaatct

base pairs


7/9

accatttagaaaaccccagtagaaactaaatctctactattagggtatgagagttaactcaatttagtcattaga

2026 to 2100

gtcgcatttcatcaagattaattaaaatttgggacctgcttcattcaagcttcatatatgctttgcagagaactc

base pairs

cagcgtaaagtagttctaattaattttaaaccctggacgaagtaagttcgaagtatatacgaaacgtctcttgag

2101 to 2175

ataaaggagcatataaggctaaatgtaaaacacaagactgtcattagaattgaattattgggcttaatataaatc

base pairs

tatttcctcgtatattccgatttacattttgtgttctgacagtaatcttaacttaataacccgaattatatttag

2176 to 2250

gtaacctatgaagtttattttctattttagttaactatgattccaattactactttgttattgtacctaagtaaa

base pairs

cattggatacttcaaataaaagataaaatcaattgatactaaggttaatgatgaaacaataacatggattcattt

2251 to 2325

ttttctttaggtcagaagcccattaaaatagttacaagcattgaacttctttagtattatattaatataaaaaca

base pairs

aaaagaaatccagtcttcgggtaattttatcaatgttcgtaacttgaagaaatcataatataattatatttttgt

2326 to 2400

tttttgtatgttttattgtaatcataaatactgctgtataaggtaataaaactctgcacctaatccccataactt

base pairs

aaaaacatacaaaataacattagtatttatgacgacatattccattattttgagacgtggattaggggtattgaa

2401 to 2475


8/9

ccagtatcattttccaattaattatcaagtctgttttgggaaacactttgaggacatttatgatgcagcagatgt

base pairs

ggtcatagtaaaaggttaattaatagttcagacaaaaccctttgtgaaactcctgtaaatactacgtcgtctaca

2476 to 2550

tgactaaaggcttggttggtagatattcaggaaatgttcactgaataaataagtaaatacattattgaaaagcaa

base pairs

actgatttccgaaccaaccatctataagtcctttacaagtgacttatttattcatttatgtaataacttttcgtt

2551 to 2625

atctgtataaatgtgaaatttttatttgtattagtaataaaacattagtagttta base pairs

tagacatatttacactttaaaaataaacataatcattattttgtaatcatcaaat 2626 to 2680

Table by Enzyme Name

Enzyme No. Positions ecognition

name c!ts o" sites se#!ence

NcoI 2 979 1834 c$catgg %ore

in"o

E&ery enzyme ana'yze( c!ts t)is se#!ence.

Table by Site Position

*!t Enzyme No. Positions ecognitionsite name c!ts o" ot)er sites se#!ence

979 NcoI 2 1834 c$catgg %ore

in"o

1834 NcoI 2 979 c$catgg %ore

in"o

,ased on the table shows that position of the cutting site of the restriction enzyme NcoI is

at the recognition sequence of **+,-- at the position site of )*) and !'($ which total

number of cut in this PAH sequence is two.

http://www.neb.com/rebase/enz/NcoI.htmlhttp://www.neb.com/rebase/enz/NcoI.htmlhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://www.neb.com/rebase/enz/NcoI.htmlhttp://www.neb.com/rebase/enz/NcoI.html


9/9

R!RN"

!. 0A1 phenylalanine hydroxylase 2 1omo sapiens -human 3

http44www.ncbi.nlm.nih.gov4gene45%5(

". 1omo sapiens phenylalanine hydroxylase -0A1& m6NA

http44www.ncbi.nlm.nih.gov4nucleotide7

cmd86etrieve9dopt8:en,ank9list;uids8$55*'!'

(. Rest!ition en$%me No/ http44www.thelabrat.com4restriction4Nco/.shtml

$. PAH &ene http'&h!.nlm.nih.&o&enePAH
http://www.ncbi.nlm.nih.gov/gene/5053http://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=4557818http://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=4557818http://www.thelabrat.com/restriction/NcoI.shtmlhttp://ghr.nlm.nih.gov/gene/PAHhttp://ghr.nlm.nih.gov/gene/PAHhttp://www.ncbi.nlm.nih.gov/gene/5053http://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=4557818http://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=4557818http://www.thelabrat.com/restriction/NcoI.shtmlhttp://ghr.nlm.nih.gov/gene/PAH

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